The most commonly reported method for synthesizing chitosan nanoparticles is ionic gelation. In this method, chitosan precursors are cross-linked by slow addition of sodium tripolyphosphate (TPP), which yields large sized (100-300 nm) particles with a high degree of polydispersity. Even though factors (such as the concentration of reactants, temperature, pH, and the level of deacetylation) governing the size and dispersivity of chitosan nanoparticles are known, understanding the process at the mechanistic level, have remained elusive. Here, we hypothesize that by using confined reaction volumes, preset temperatures and predefined reaction times, it should be possible to exert control over the kinetics of nanoparticles synthesis. This led to design and fabrication of a polydimethylsiloxane microreactor with magnetic micro needles for the synthesis of monodisperse chitosan nanoparticles. The well- controlled microreactor-based mixing generated monodisperse particles with tunable properties including antifungal drug entrapment, release rate, and effective activity against Candida.